Measuring progress in Premo order-verification

Since verification of computational simulation codes requires significant resources, the ability to measure progress in verification is critical to assess whether resources are being applied appropriately. Additionally, potential users need to know what fraction of the software has been order-verified. In this study, the procedures and progress measures presented by Knupp et al. (Measuring progress order-verification within software development projects. Engineering with Computers, appears in this issue, 2007) are demonstrated on the Premo software, which simulates compressible aerodynamics through and around general geometries. Premo was selected for this demonstration because extensive order-verification tests have been previously performed, yet no systematic effort has been made to assess test-suite completeness or progress. This effort was performed to identify the practical issues encountered when attempting to apply the ideas by Knupp (Measuring progress order-verification within software development projects. Engineering with Computers, appears in this issue, 2007) to existing production-quality software. In this work, a non-specific order-verification exercise is considered, as opposed to an application-specific order-verification exercise, since past and present Premo order-verification efforts have been motivated by the need to verify all of the code, rather than portions relevant for specific applications. Constructing an order-verification test suite that verifies the order of accuracy of all the code capabilities is a major step in measuring progress. A practical approach to test-suite construction is described that helps create a complete test suite through a combination of coarse-grain code coverage, input-keyword inspection, discretization-algorithm documentation, and expert knowledge. Some of the difficulties and issues encountered during the construction of the test suite are described, along with recommendations on how to deal with them. Once the test suite is constructed, the progress measures proposed by Knupp (Measuring progress order-verification within software development projects. Engineering with Computers, appears in this issue, 2007) can be evaluated and used to reconstruct the history of progress in Premo verification over the past several years. Gaps in Premo verification are identified and indicate future directions for making progress. Additionally, a measure of Premo verification fitness is computed for selected applications commonly simulated in the aerospace industry. It is hoped that this demonstration will provide a practical example for other software-development groups in measuring their own verification progress. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed-Martin Company, for the United States Department of Energy’s National Nuclear Security Administration under Contract DE-AC04-94AL85000.

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On the pH dependence of protein stability

This paper treats the free energy contribution of ionizable groups to protein stability. A method is presented for the calculation of the pH dependence of the denaturation free energy of a protein, which yields results that can be compared directly to experiment. The first step in the treatment is the determination of the average charges of all the ionizable groups in both the folded and unfolded protein. An expression due to Tanford then relates the pH dependence of the unfolding free energy to the difference in net charge between the two states. In order to determine absolute rather than relative unfolding free energies, it is necessary to calculate the total contribution of ionizable groups to protein stability at some reference pH. This is accomplished through a statistical mechanical treatment similar to the one used previously in the calculation of pKas. The treatment itself is rigorous but it suffers from uncertainties in the pKa calculations. Nevertheless, the overall shape of experimentally observed plots of denaturation free energy as a function of pH are reasonably well reproduced by the calculations. A number of general conclusions that arise from the analysis are: (1) knowledge of titration curves and/or effective pKa values of ionizable groups in proteins is sufficient to calculate the pH dependence of the denaturation free energy with respect to some reference pH value. However, in order to calculate the absolute contribution of ionizable groups to protein stability, it is necessary to also know the intrinsic pKa of each group. This is defined as the pKa of a group in a hypothetical state of the protein where all other groups are neutral. (2) Due to desolvation effects, ionizable groups destabilize proteins, although the effect is strongly dependent on pH. There are however, strongly stabilizing pairwise Coulombic interactions on the surface of proteins. (3) Plots of stability versus pH should not be interpreted in terms of a group whose pKa corresponds to the titration midpoint, but rather to a group with different pKas (that correspond approximately to the titration end points) in each state. (4) Any residual structure in the GuHCl-denatured state of proteins appears to have little effect on the pH dependence of stability. (5) pH-dependent unfolding, for example to the "molten globule" state, appears due to individual groups with anomalous pKas whose locations on the protein surface may determine the nature of the unfolded state.     

Risk from relativistic heavy ions on manned space missions

The risk from exposure to radiation posed to space travelers outside the magnetic shielding provided by the geomagnetosphere will come from two sources: the slowly varying but low intensity high-energy galactic cosmic rays and the more intense predominantly low-energy protons from large solar particle events associated with magnetic disturbances originating sporadically on or within the solar surface during the active period of the 11-year solar cycle. The energy spectra of the protons in solar particle events are quite soft, with large numbers of low-energy protons and a rather steep decrease of the energy spectra with increasing energy. This allows for the possibility to provide, within the space vehicle or habitat, a well-shielded area sometimes called a "storm shelter" or "safe haven" where the travelers could gather during the largest particle events. Intensity risetimes on the order of half an hour or more and overall event durations of 1 to 2 days would make actively seeking a well-shielded shelter for the duration a distinct possibility. The high-energy and penetrating nature and relative constancy of the galactic cosmic rays, on the other hand, do not allow the use of highly shielded areas as a means of protection against them. The first question to answer becomes: what is the risk to human health from the galactic cosmic rays? We need to have a good idea of the answer to this question before we can address the problem of how to best protect human health or, indeed, whether any specific measures need to be taken.     

View angle effects on MODIS snow mapping in forests

Binary snow maps and fractional snow cover data are provided routinely from MODIS (Moderate Resolution Imaging Spectroradiometer). This paper investigates how the wide observation angles of MODIS influence the current snow mapping algorithm in forested areas. Theoretical modeling results indicate that large view zenith angles (VZA) can lead to underestimation of fractional snow cover (FSC) by reducing the amount of the ground surface that is viewable through forest canopies, and by increasing uncertainties during the gridding of MODIS data. At the end of the MODIS scan line, the total modeled error can be as much as 50% for FSC. Empirical analysis of MODIS/Terra snow products in four forest sites shows high fluctuation in FSC estimates on consecutive days. In addition, the normalized difference snow index (NDSI) values, which are the primary input to the MODIS snow mapping algorithms, decrease as VZA increases at the site level. At the pixel level, NDSI values have higher variances, and are correlated with the normalized difference vegetation index (NDVI) in snow covered forests. These findings are consistent with our modeled results, and imply that consideration of view angle effects could improve MODIS snow monitoring in forested areas.     

Modeling broad-scale patterns of avian species richness across the Midwestern United States with measures of satellite image texture

Avian biodiversity is threatened, and in order to prioritize limited conservation resources and conduct effective conservation planning a better understanding of avian species richness patterns is needed. The use of image texture measures, as a proxy for the spatial structure of land cover and vegetation, has proven useful in explaining patterns of avian abundance and species richness. However, prior studies that modeled habitat with texture measures were conducted over small geographical extents and typically focused on a single habitat type. Our goal was to evaluate the performance of texture measures over broad spatial extents and across multiple habitat types with varying levels of vertical habitat structure. We calculated a suite of texture measures from 114 Landsat images over a study area of 1,498,000 km² in the Midwestern United States, which included habitats ranging from grassland to forest. Avian species richness was modeled for several functional guilds as a function of image texture. We subsequently compared the explanatory power of texture-only models with models fitted using landscape composition metrics derived from the National Land Cover Dataset, as well as models fitted using both texture and composition metrics. Measures of image texture were effective in modeling spatial patterns of avian species richness in multiple habitat types, explaining up to 51% of the variability in species richness of permanent resident birds. In comparison, landscape composition metrics explained up to 56% of the variability in permanent resident species richness. In the most heavily forested ecoregion, texture-measures outperformed landscape metrics, and the two types of measurements were complementary in multivariate models. However, in two out of three ecoregions examined, landscape composition metrics consistently performed slightly better than texture measures, and the variance explained by the two types of measures overlapped considerably. These results show that image texture measures derived from satellite imagery can be an important tool for modeling patterns of avian species richness at broad spatial extents, and thus assist in conservation planning. However, texture measures were slightly inferior to landscape composition metrics in about three-fourths of our models. Therefore texture measures are best considered in conjunction with landscape metrics (if available) and are best used when they show explanatory ability that is complementarity to landscape metrics.     

A Digitally Controlled Stimulator for Neurophysiological Applications

A stimulator circuit is presented which is capable of generating pulse train waveforms suitable for neurophysiological experiments are available, as well as special test conditions such as dishabituation. Digital and linear integrated circuits are used to provide precise control over the stimulus parameters.     

A complete parameterization of clf‐based input‐to‐state stabilizing control laws

Sontag's formula proves constructively that the existence of a control Lyapunov function implies asymptotic stabilizability. A similar result can be obtained for systems subject to unknown disturbances via input‐to‐state stabilizing control Lyapunov functions (ISS‐clfs) and the input‐to‐state analogue of Sontag's formula. The present paper provides a generalization of the ISS version of Sontag's formula by completely parameterizing all continuous ISS control laws that can be generated by a known ISS‐clf. When a simple inner‐product constraint is satisfied, this parameterization also conveniently describes a large family of ISS controls that solve the inverse‐optimal gain assignment problem, and it is proved that these controls possess Kalman‐type gain margins. Copyright © 2004 John Wiley & Sons, Ltd.     

Simultaneous structure and elastic wave velocity measurement of SiO2 glass at high pressures and high temperatures in a Paris-Edinburgh cell

An integration of multi-angle energy-dispersive x-ray diffraction and ultrasonic elastic wave velocity measurements in a Paris-Edinburgh cell enabled us to simultaneously investigate the structures and elastic wave velocities of amorphous materials at high pressure and high temperature conditions. We report the first simultaneous structure and elastic wave velocity measurement for SiO(2) glass at pressures up to 6.8 GPa at around 500°C. The first sharp diffraction peak (FSDP) in the structure factor S(Q) evidently shifted to higher Q with increasing pressure, reflecting the shrinking of intermediate-range order, while the Si-O bond distance was almost unchanged up to 6.8 GPa. In correlation with the shift of FSDP position, compressional wave velocity (Vp) and Poisson's ratio increased markedly with increasing pressure. In contrast, shear wave velocity (Vs) changed only at pressures below 4 GPa, and then remained unchanged at ~4.0-6.8 GPa. These observations indicate a strong correlation between the intermediate range order variations and Vp or Poisson's ratio, but a complicated behavior for Vs. The result demonstrates a new capability of simultaneous measurement of structures and elastic wave velocities at high pressure and high temperature conditions to provide direct link between microscopic structure and macroscopic elastic properties of amorphous materials.     

Computer-aided procedures for subdivision design and evaluation

Design and management of residential subdivisions are described using a case study in Regina, Saskatchewan. Capital, operation and maintenance costs of physical services and fuel costs for intra-subdivision trips are compared for four subdivision layouts using the procedures. The solar superblock layout is the lowest subdivision layout. Future procedures to assist subdivision design engineers and planners are summarized.     

Term distribution visualizations with Focus+Context

Many text searches are meant to identify one particular fact or one particular section of a document. Unfortunately, predominant search paradigms focus mostly on identifying relevant documents and leave the burden of within-document searching on the user. This research explores term distribution visualizations as a means to more clearly identify both the relevance of documents and the location of specific information within them. We present a set of term distribution visualizations, introduce a Focus+Context model for within-document search and navigation, and describe the design and results of a 34-subject user study. This user study shows that these visualizations—with the exception of the grey scale histogram variant—are comparable in usability to our Grep interface. This is impressive given the substantial experience of our users with Grep functionality. Overall, we conclude that user do not find this visualization model difficult to use and understand.